Chapter 9, Molecular Structure of DNA and RNA

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The key takeaways are that DNA carries genetic information and helps organisms fight entropy by storing information and building complex structures using energy from the sun.

DNA carries genetic information that is passed from parents to offspring and allows for variation between organisms.

Living organisms obtain energy from the sun and use it to build complex structures and replicate, fighting the natural increase in entropy of the universe.

LECTURE 1

Introduction to
DNA and RNA
(Chapter 09)
Slides 1-25; 35-48; 54-57
On your own:
Slides 26-34; 49-53; 58-62

1
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INTRODUCTION
Genetics: Study of the structure, function,
transmission of genes
Only living organisms have genes
To understand genetics, we will start with the
question: What is Life?
Characteristics shared by all living forms but not by
non-living forms

What is the role of DNA in life?


DNA carries information
Information, entropy and Solla Sollew
Duhka (A wheel out of kilter)
I Had Trouble in Getting to Solla Sollew (where there arent any
problems at least very few)

UNIVERSE

LIFE (GENES)

(entropy)

(negative entropy)

How does life fight entropy?


Living organisms suck energy (directly or
indirectly) from the Sun
If no life, medium =
medium radiation
energy, medium
entropy

If life, long = low


radiation energy
high entropy

Short mean = high


radiation energy, low
entropy
Very high
potential energy;
Very low entropy
4

Fusion reactions in suns core


Hydrogen to helium with release of photons

Mass converted to energy (E = mc2)


600 million tons hydrogen fused to helium per second
Creates 596 tons helium per second + 3.9 x 10 26 Joules of energy
Life borrows this energy to build complex, highly ordered structures

The source of all lifes problems is entropy


The solution is stored as information in DNA
Information and negative entropy
Analog vs digital

Different organisms have different genes;


different strategies for the survival of the genes
and their transmission to the next generation
Those genes that built the best survival
machines are still with us today
The vast majority of genes were lost
This is a blind, undirected process
6

MOLECULAR GENETICS
Chapter 9 examines the genetic material in detail:
molecular genetics
The study of DNA structure and function at the
molecular level

Recent dramatic advances in techniques and


approaches have greatly expanded our
understanding of molecular genetics
And also of transmission and population genetics

To a large extent, our knowledge of genetics


comes from our knowledge of the molecular
structure of DNA and RNA
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9.1 IDENTIFICATION OF DNA AS


THE GENETIC MATERIAL
To fulfill its role, the genetic material must meet
several criteria
1. Information: It must contain the information necessary
to make an entire organism
2. Transmission: It must be passed from parent to
offspring
3. Replication: It must be copied
In order to be passed from parent to offspring

4. Variation: It must be capable of changes


To account for the known phenotypic variation in each species
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9.1 IDENTIFICATION OF DNA AS


THE GENETIC MATERIAL
The data of many geneticists, including
Mendel, were consistent with these four
properties
However, the chemical nature of the genetic material
cannot be identified solely by genetic crosses

Indeed, the identification of DNA as the genetic


material involved a series of outstanding
experimental approaches
These will be examined next
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Frederick Griffith Experiments with


Streptococcus pneumoniae
Griffith studied a bacterium (pneumococci) now
known as Streptococcus pneumoniae
S. pneumoniae comes in two strains
S Smooth
Secrete a polysaccharide capsule
Protects bacterium from the immune system of animals

Produce smooth colonies on solid media

R Rough
Unable to secrete a capsule
Produce colonies with a rough appearance
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10

In 1928, Griffith conducted experiments using two


strains of S. pneumoniae: type IIIS and type IIR

1. Inject mouse with live type IIIS bacteria

2. Inject mouse with live type IIR bacteria

Mouse survived
No living bacteria isolated from the mouses blood

3. Inject mouse with heat-killed type IIIS bacteria

Mouse died
Type IIIS bacteria recovered from the mouses blood

Mouse survived
No living bacteria isolated from the mouses blood

4. Inject mouse with live type IIR + heat-killed type IIIS cells

Mouse died
Type IIIS bacteria recovered from the mouses blood
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11

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Living type S bacteria were


injected into a mouse.

Living type R bacteria were


injected into a mouse.

Heat-killed type S bacteria


were injected into a mouse.

Living type R and heat-killed


type S bacteria were injected
into a mouse.
Live
type R

Dead
type S

After
several
days

Mouse died

After
several
days

Mouse survived

After
several
days

Mouse survived

After
several
days

Mouse died

Type S bacteria were isolated


from the dead mouse.

No living bacteria were isolated


from the mouse.

No living bacteria were isolated


from the mouse.

Type S bacteria were isolated


from the dead mouse.

(a) Live type S

(b) Live type R

(c) Dead type S

(d) Live type R + dead type S

Figure 9.1

12

Griffith concluded that something from the dead


type IIIS bacteria was transforming type IIR
bacteria into type IIIS

He called this process transformation

The substance that allowed this to happen was


termed the transformation principle

Griffith did not know what it was


Suggested that the genetic information molecule is
resistant to high temperature
Most proteins degrade at high temperature
Connect Griffiths experiment to Experiment 1 (lab)
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13

We now know that the formation of the capsule is


guided by the bacterias genetic material

Transformed R bacteria acquired a gene from the dead


lysed S bacterua that directs the cell how to make a
capsule polysachharide
Variation exists in ability to make capsule (R cells carry a
non-function allele for the gene)
The gene required to create a capsule is replicated and
transmitted from mother to daughter cells
Once R cells acquired it they passed the trait to their
offspring

The molecular nature of the transforming principle


was determined using experimental approaches
that incorporated various biochemical techniques
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14

The Experiments of
Avery, MacLeod and McCarty
Avery, MacLeod and McCarty realized that Griffiths
observations could be used to identify the genetic material
They carried out their experiments in the 1940s
At that time, it was known that DNA, RNA, proteins and
carbohydrates are the major constituents of living cells

They prepared cell extracts from type IIIS cells and purified
each type of macromolecule
Only the extract that contained purified DNA was able to convert
type IIR bacteria into type IIIS
Treatment of the DNA extract with RNase or protease did not
eliminate transformation
Treatment with DNase did
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15

Figure 9.2

Avery et al. conducted the following experiments

To further verify that DNA, and not a contaminant (RNA


or protein), is the genetic material

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Type R
cells

Type S
DNA
extract

Type R
cells

Mix

Type S
DNA
extract
+
DNase

Type R
cells

Mix

Type S
DNA
extract
+
RNase

Type R
cells

Mix

Type R
cells

Type S
DNA
extract
+
protease
Mix

Allow sufficient time for the DNA to be taken up by the type R bacteria. Only a small percentage of the type R bacteria will be transformed to type S.
Add an antibody that aggregates type R bacteria (that have not been transformed). The aggregated bacteria are removed by gentle centrifugation.
Plate the remaining bacteria on petri plates. Incubate overnight.

Transformed

Transformed

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Transformed

16

Experiment 9A Hershey and Chase


Experiment with Bacteriophage T2
In 1952, Alfred Hershey and Marsha Chase
provided further evidence that DNA is the genetic
material
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They studied the


bacteriophage T2

Figure 9.3

It is relatively simple
since its composed of
only two
macromolecules

DNA and protein

DNA
(inside the
capsid head)

Inside the
capsid

Head
Sheath

Made up
of protein

Tail fiber

Base plate

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17

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Phage binds to host cell.
Capsid
Genetic material
Bacterial
cell wall
Bacterial
chromosome

Phage injects its


DNA into host cell.

Figure 9.4

Phage coat (protein)


precariously attached
to bacterial cell

The expression of
phage genes leads
to the synthesis of
phage components.

Life cycle of
bacteriophage T2

DNA inside of cell


Phage components
are assembled.

Host cell lyses


and new phages
are released.

18

The Hershey and Chase experiment can be


summarized as follows:
Used radioisotopes to distinguish DNA from proteins
32P labels DNA specifically
35S labels protein specifically
Radioactively-labeled phages were used to infect
non-radioactive Escherichia coli cells
After allowing sufficient time for infection to proceed,
the residual phage particles were sheared off the cells
=> Phage ghosts and E. coli cells were separated
Radioactivity was monitored using a scintillation
counter
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19

9-14

The Hypothesis
Only the genetic material of the phage is injected
into the bacterium
Isotope labeling will reveal if it is DNA or protein

Testing the Hypothesis

Refer to Figure 9.5

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20

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Experimental level
Conceptual level
1.Grow bacterial cells. Divide into
two flasks.

Suspension of
E. coli cells

S-labeled
protein capsid
35

P-labeled
DNA
32

2.Into one flask, add 35S-labeled phage; in


the second flask, add 32P-labeled phage.

S-labeled
T2 phage
35

P-labeled
T2 phage
32

3.Allow infection to occur.


After blending
4.Agitate solutions in blenders for
different lengths of time to shear the
empty phages off the bacterial cells.
Suspension of Suspension of
E. coli infected with
E. coli infected with
35
S-labeled phage32P-labeled phage
5.Centrifuge at 10,000 rpm.
Supernatant
6.The heavy bacterial cells sedimentwith
to the
35
pellet, while the lighter phages remain
in
S-labeled
the supernatant. (See Appendix for
empty phage
explanation of centrifugation.)
Pellet with
unlabeled
DNA in
infected
E. coli cells
7.Count the amount of radioisotope in
the supernatant with a Geiger counter.
Compare it with the starting amount.

Figure 9.5

Supernatant
with
unlabeled
empty phage
Pellet with
32
P-labeled
DNA in
infected
E. coli cells

Bacterial cell
Viral genetic
material
Sheared empty
phage (labeled)
Bacterial
cell
Viral
genetic
material
(labeled)
Sheared
empty
phage
Sheared empty
phages (labeled)
Sheared
empty
phages
(unlabeled)

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21

The Data
Total isotope in supernatant (%)

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100
80

Extracellular 35S

80%
Blending removes 80%
of 35S from E. coli cells.

Extracellular 32P

35%
Most of the 32P (65%)
remains with intact
E. coli cells.

60
40
20
0

Agitation time in blender (min)


Data from A. D. Hershey and Martha Chase (1952) Independent Functions of Viral Protein and Nucleic Acid in Growth of
Bacteriophage. Journal of General Physiology 36, 3956.

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22

Interpreting the Data

Most of the 35S was found


in the supernatant

But only a small


percentage of 32P

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Total isotope in supernatant (%)

100
80

Extracellular 35S

80%
Blending removes 80%
of 35S from E. coli cells.

Extracellular 32P

35%
Most of the 32P (65%)
remains with intact
E. coli cells.

60
40
20
0

Agitation time in blender (min)


Data from A. D. Hershey and Martha Chase (1952) Independent Functions of Viral Protein and Nucleic Acid in Growth of
Bacteriophage. Journal of General Physiology 36, 3956.

These results suggest that DNA is injected into the bacterial cytoplasm
during infection
Data is not conclusive since less than 100% of the DNA or protein
ended up in the cell or supernatant
Data is consistent with the hypothesis that DNA is the genetic
material
23

9-18

RNA Functions as the Genetic Material


in Some Viruses

In 1956, A. Gierer and G. Schramm isolated RNA


from the tobacco mosaic virus (TMV), a plant virus

Purified RNA caused the same lesions as intact TMV


viruses

Therefore, the viral genome is composed of RNA

Since that time, many RNA viruses have been


found

Refer to Table 9.1

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24

25

9.2 NUCLEIC ACID


STRUCTURE On Your Own
DNA and RNA are large macromolecules with
several levels of complexity
1. Nucleotides form the repeating unit of nucleic acids
2. Nucleotides are linked to form a linear strand of
RNA or DNA
3. Two strands can interact to form a double helix
4. The 3-D structure of DNA results from folding and
bending of the double helix. Interaction of DNA with
proteins produces chromosomes within living cells
Refer to fig. 9.6
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26

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Nucleotides
A

TC

AA

TC

AA

TC

AAT

Single strand

C
G

C A
T GT
T A
A

G T
A C
GA
T

C A
T GT
T A
A

Double helix

Figure 9.6

Three-dimensional structure

27

Nucleotides

The nucleotide is the repeating structural unit of


DNA and RNA

It has three components

A phosphate group
A pentose sugar
A nitrogenous base

Refer to Figure 9.7


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28

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Bases
Phosphate group

Sugars
5

HOCH2
4

O
CH3

1N

D-Deoxyribose (in DNA)

H
3

HO

OH

D-Ribose (in RNA)

N
H

3N
2

Adenine (A)

OH

1N

4
1

3N
2

Uracil (U) (in RNA)

NH 2
H

NH2

Thymine (T) (in DNA)

HOCH2

Figure 9.7

HO
O

Pyrimidines
(single ring)

NH2

OH

Purines
(double ring)

5
6

4
1

3N
2

H
Guanine (G)

Cytosine (C)

29

9-24

These atoms are found within individual nucleotides

However, they are removed when nucleotides join together to make


strands of DNA or RNA
A, G, C or T

A, G, C or U

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O
O P

Base
O

O
Phosphate

CH2

5
4

H
3

H
2

OH
H
Deoxyribose

(a) Repeating unit of


deoxyribonucleic
acid (DNA)
Figure 9.8

Base
O

O
Phosphate

CH2

H
3

O
H
2

OH
OH
Ribose

(b) Repeating unit of


ribonucleic acid (RNA)

The structure of nucleotides found in (a) DNA and (b) RNA


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30

Base + sugar nucleoside

Base + sugar + phosphate(s) nucleotide

Example
Adenine + ribose = Adenosine
Adenine + deoxyribose = Deoxyadenosine

Example
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)

Refer to Figure 9.9


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31

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Adenosine triphosphate

Adenosine diphosphate
Adenosine monophosphate
Adenosine
Adenine

Phosphoester bond

NH2

H
O
O

P
O

O
O

O
O

N
O

Phosphate groups
Phosphates are
attached here

Figure 9.9

CH2

5
4

HO

Ribose

N
Base always
attached here

OH

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32

Nucleotides are covalently linked together by


phosphodiester bonds

Therefore the strand has directionality

A phosphate connects the 5 carbon of one nucleotide to


the 3 carbon of another
5 to 3
In a strand, all sugar molecules are oriented in the same
direction

The phosphates and sugar molecules form the


backbone of the nucleic acid strand

The bases project from the backbone


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33

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Backbone

Bases
O

CH3
H

O
O

CH2
5
4
H
H

O
1
H
2
H
H

Phosphodiester
linkage

Thymine (T)

NH2
N

H
N

O
O

CH2
5
4
H
H

1
H
2
H
H

NH2
H

O
P

Adenine (A)

CH2
5
4
H
H

Cytosine (C)
O

O
1
H
2
H
H

Guanine (G)
O
N

H
N

Single
nucleotide

CH2
5
O
4
H
Phosphate H

3
OH

Figure 9.10

NH2

O
1
H
2
H
H

Sugar (deoxyribose)

34

A Few Key Events Led to the Discovery of


the Structure of DNA

In 1953, James Watson and Francis Crick elucidated


the double helical structure of DNA

The scientific framework for their breakthrough was


provided by other scientists including

Linus Pauling
Rosalind Franklin and Maurice Wilkins
Erwin Chargaff

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Linus Pauling

In the early 1950s, he


proposed that regions of
protein can fold into a
secondary structure

-helix

N C C

O
N

HO

O N
H
N

C
H

N
C

Carbonyl
oxygen

Amide
hydrogen

O N

To elucidate this structure,


he built ball-and-stick
models

O
Hydrogen
bond

C
H

O
N

N
C

Figure 9.11

(a) An helix in a protein


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36

Rosalind Franklin

She worked in the


same laboratory as
Maurice Wilkins
She used X-ray
diffraction to study
wet fibers of DNA

X rays diffracted
by DNA
Wet DNA fibers
X-ray beam

The pattern represents the


atomic array in wet fibers.

(b) X-ray diffraction of wet DNA fibers

Figure 9.12b

The diffraction pattern is interpreted


(using mathematical theory)
This can ultimately provide
information concerning the
structure of the molecule

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37

Rosalind Franklin

She made marked advances in X-ray diffraction


techniques with DNA

The diffraction pattern she obtained suggested


several structural features of DNA

Helical
More than one strand
10 base pairs per complete turn

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38

Erwin Chargaffs Experiment

Chargaff pioneered many of the biochemical


techniques for the isolation, purification and
measurement of nucleic acids from living cells

It was known that DNA contained the four bases:


A, G, C and T

Chargaff analyzed the base composition of DNA


isolated from many different species
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39

The Hypothesis
An analysis of the base composition of DNA in
different species may reveal important features
about the structure of DNA

Testing the Hypothesis

Refer to Figure 9.13

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40

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y
Conceptual level

Experimental level
Solution of
1. For each type of cell, extract the
chromosomal
chromosomal material. This can be extract
done in a variety of ways, including the
use of high salt, detergent, or mild alkali
treatment. Note: The chromosomes
contain both DNA and protein.

2. Remove the protein. This can be done in


several ways, including treament with
protease.

3. Hydrolyze the DNA to release the bases


from the DNA strands. A common way
to do this is by strong acid treatment.

DNA +
proteins

Protease

DNA

Acid

4. Separate the bases by chromatography.


Paper chromatography provides an easy
way to separate the four types of bases.
(The technique of chromatography is
described in the Appendix.)
5. Extract bands from paper into solutions
Origin
and determine the amounts of each base
by spectroscopy. Each base will absorb
light at a particular wavelength. By
examining the absorption profile of a
sample of base, it is then possible to
calculate the amount of the base.
(Spectroscopy is described in the
Appendix.)

Figure 9.13

AA A

A A
C

C C C CC C

G
G G GG G
TT

Individual
bases

G
T

6. Compare the base content in the DNA


from different organisms.

41

The Data

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42

Interpreting the Data

The data shown in Figure 9.13 are only a small


sampling of Chargaffs results

The compelling observation was that

Percent of adenine = percent of thymine


Percent of cytosine = percent of guanine

This observation became known as Chargaffs rule

It was a crucial piece of evidence that Watson and Crick


used to elucidate the structure of DNA
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43

Watson and Crick

Familiar with all of these key observations, Watson


and Crick set out to solve the structure of DNA

They tried to build ball-and-stick models that incorporated


all known experimental observations

A critical question was how the two (or more strands)


would interact

An early hypothesis proposed that DNA strands interact


through phosphate-Mg++ cross-links
Refer to Figure 9.14
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44

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Base

Base
Sugar

Sugar
O

Base

O
P

O
Sugar

Mg2+

Base

P
O

O
Sugar

Figure 9.14

This hypothesis was, of course, incorrect!


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45

Watson and Crick

They went back to the ball-and-stick units


They then built models with the

They first considered a structure in which bases form


H bonds with identical bases in the opposite strand

Sugar-phosphate backbone on the outside


Bases projecting toward each other

ie., A to A, T to T, C to C, and G to G

Model building revealed that this also was incorrect


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46

Watson and Crick

They then realized that the hydrogen bonding of A to


T was structurally similar to that of C to G

So they built ball-and-stick models with AT and CG


interactions between the two DNA strands

These were consistent with all known data about DNA structure

Refer to Figure 9.15

Watson, Crick and Maurice Wilkins were awarded


the Nobel Prize in 1962

Rosalind Franklin died in 1958, and Nobel prizes are not


awarded posthumously
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47

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Barrington Brown/Photo Researchers

(a) Watson and Crick

Figure 9.15

Hulton|Archive by Getty Images

(b) Original model of the DNA double helix

48

The DNA Double Helix


On Your Own

General structural features (Figures 9.16 & 9.17)

Two strands are twisted together around a


common axis
There are 10 bases and 3.4 nm per complete turn
of the helix
The two strands are antiparallel

One runs in the 5 to 3 direction and the other 3 to 5

The helix is right-handed

As it spirals away from you, the helix turns in a


clockwise direction
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49

The DNA Double Helix

General structural features (Figures 9.16 & 9.17)

The double-bonded structure is stabilized by

1. Hydrogen bonding between complementary bases

A bonded to T by two hydrogen bonds


C bonded to G by three hydrogen bonds

2. Base stacking

Within the DNA, the bases are oriented so that the flattened
regions are facing each other

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50

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2 nm

Key Features

5 P 3
S P
P
A S

Two strands of DNA form a


right-handed double helix.
The bases in opposite strands
hydrogen bond according to the
AT/GC rule.

The 2 strands are antiparallel with


regard to their 5 to 3 directionality.

G
G

S
C

P S

There are ~10.0 nucleotides in each


P S
P
strand per complete 360 turn of
S P
the helix.
S
A T S
C

P
P
S
S

T
P

Figure 9.16

C
P

O P

N
O

3 end
HO

HH

H
O

CH2
H

NH2

H
N

P S

O P

CH2
H

H H
N

HH

CH2 O P

N
O

H2N

CH3

O
H

G S

H2N

H H
N

H H

H
O

CH2 O P O
O

H N

O P

One nucleotide
0.34 nm

O
O

CH2
H

H
OH

H2N

N H

NH2

3 end
S

CH2 O P
O

C P

P S
C

P S
PS
P

S C
S

CH2

NH2

G
A

O P O

CH3

O
O

T
A
P
G
S
P

5 end

One complete
turn 3.4 nm

H
N

H H

H
H

CH2 O P
O

5 end

3
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51

The DNA Double Helix

General structural features (Figures 9.16 & 9.17)

There are two asymmetrical grooves on the


outside of the helix

1. Major groove

2. Minor groove

Certain proteins can bind within these grooves

They can thus interact with a particular sequence of bases

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52

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Minor
groove

Minor
groove

Major
groove

Major
groove
Laguna Design/Photo Researchers

(a) Ball-and-stick model of DNA

Figure 9.17

(b) Space-filling model of DNA

53

To calculate how often the enzyme will


cut:
4(# bp in recognition site)
For Eco RI = 46 = cuts every 4,096 bp

Homodimerizes then binds in


successive major grooves to cut
each DNA strand

To calculate number of cuts/genome:


(bp in genome)/4(# bp in recognition site)
Eco RI cuts the human genome:
(3.2 x 109 bp)/4096 cuts/bp = 780,000
cuts
54

The Three-Dimensional Structure of


DNA

To fit within a living cell, the DNA double helix must


be extensively compacted into a 3-D conformation

This is aided by DNA-binding proteins

Refer to 9.20

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55

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Radial loops
(300 nm in diameter)

Metaphase
chromosome
30 nm fiber

Nucleosomes
(11 nm in diameter)
DNA
(2 nm in diameter)

Histone
protein

DNA wound
around histone
proteins

Each chromatid
(700 nm in diameter)

Figure 9.20

56

57

RNA Structure On Your Own

The primary structure of an RNA strand is much


like that of a DNA strand

Refer to Figure 9.21 vs. 9.10

RNA strands are typically several hundred to


several thousand nucleotides in length

In RNA synthesis, only one of the two strands of


DNA is used as a template
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58

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Backbone

Bases
O

H
O
O

P
O

5
4

CH2
H

Uracil (U)
O

1
H
2
OH

Phosphodiester
linkage

NH2
N

H
N

O
O

P
O

5
4

CH2
H

Adenine (A)

O
1
H
2
OH

NH2
H

O
O

5
4

CH2

Cytosine (C)

1
H

Guanine
(G)

2
OH

H
N

RNA
nucleotide

Phosphate

Figure 9.21

5
4

CH2
H

NH2

3
OH

Sugar (ribose)

1
H

2
OH

59

Although usually single-stranded, RNA molecules


can form short double-stranded regions

This secondary structure is due to complementary basepairing

This allows short regions to form a double helix

RNA double helices typically

A to U and C to G

Are right-handed
Have the A form with 11 to 12 base pairs per turn

Different types of RNA secondary structures are


possible

Refer to Figure 9.22


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60

Complementary regions
Held together by
hydrogen bonds

Figure 9.22

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U
U A

A
A U
U A

G C
C G
C G

C
A

A U
(a) Bulge loop

U
G

C G
C G

C
U A
C G

G C A A G
G
C
U U C

A
C

C C G A A
G G
C U U

G C
A U
A U

C G

(c) Multibranched junction

Non-complementary regions
Have bases projecting away
from double stranded regions

C G

G C
A U
A U

C G

C G

(b) Internal loop

C G

A U

U A

A
G

G C
A U

C
U
A
G
G
U
C A

C
G G
A
C C G U

(d) Stem-loop

Also called
hair-pin

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61

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Double helix

Many factors
contribute to the
tertiary structure of
RNA

5 end

Molecule contains
single- and doublestranded regions

For example

Base-pairing and
base stacking within
the RNA itself
Interactions with
ions, small
molecules and large
proteins

3 end
(acceptor
site)

Double helix

These spontaneously
fold and interact to
produce this 3-D
structure

Anticodon
(a) Ribbon model

Figure 9.23

Figure 9.23 depicts the tertiary structure of tRNAphe

The transfer RNA that carries phenylalanine


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Animations

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viewed in Presentation Mode (Slide
Show view). You may see blank slides
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